├── .gitignore ├── BAT └── README ├── GWAS ├── Hudson_Plot.ipynb ├── LD_Clumping.ipynb ├── LMM.ipynb ├── MTAG.ipynb ├── README.md ├── Region_Extraction.ipynb ├── data │ ├── README.md │ ├── boltlmm_template.yml │ ├── fastGWA_template.yml │ ├── gcta-cojo_template.yml │ ├── gmmat_template.yml │ ├── meta_template.yml │ ├── mtag_template.yml │ ├── regenie_template.yml │ └── smmat_template.yml ├── liftover.ipynb ├── lmm.dockerfile └── marp.dockerfile ├── LDSC ├── Deep_Learning │ ├── LDSC_DeepSea_Minimal_Example.ipynb │ ├── LDSC_DeepSea_Minimal_Example.sos │ ├── ReadME.md │ └── all_neuron_tutorial.yml ├── LDSC.ipynb ├── LDSC.sos ├── LDSC_Code.ipynb └── LDSC_Code.sos ├── PoPS ├── pops.ipynb └── utils.R ├── README.md ├── admin ├── Job_Example.ipynb ├── csg.yml ├── farnam.yml ├── midway2.yml └── submit_csg.ipynb ├── config.yml ├── docs ├── GWAS.tpl ├── GWAS │ ├── GWAS_QC.html │ ├── Hudson_Plot.html │ ├── LD_Clumping.html │ ├── LMM.html │ ├── PCA.html │ └── Region_Extraction.html ├── MANIFEST ├── css │ ├── cerulean.css │ ├── flatly.css │ ├── jt.css │ ├── readable.css │ ├── testtab.css │ └── toc2.css ├── fine-mapping.tpl ├── fine-mapping │ ├── SuSiE_RSS.html │ ├── SuSiE_RSS_before_initialization.html │ ├── finemapping_results_wrangler.html │ ├── finemapping_to_ldsc.pipeline.html │ ├── gwas_enrichment.html │ ├── summary_statistics_finemapping.html │ └── summary_statistics_wrangler.html ├── fonts │ ├── droid-sans.ttf │ ├── firacode.otf │ └── ptmono.ttf ├── index.html ├── index.tpl ├── ipynb_workflowr.sos ├── jnbinder.py ├── js │ ├── doc_toc.js │ ├── docs.js │ └── sha1.js ├── ldpred.tpl ├── ldpred │ ├── index.html │ └── ldpred2_example.html ├── multivariate-fine-mapping.tpl ├── multivariate-fine-mapping │ ├── mixture_prior.html │ └── mvSuSiE.html ├── search.html ├── site_libs │ ├── bootstrap-3.3.5 │ │ ├── css │ │ │ ├── bootstrap-theme.css │ │ │ ├── bootstrap-theme.css.map │ │ │ ├── bootstrap-theme.min.css │ │ │ ├── bootstrap.css │ │ │ ├── bootstrap.css.map │ │ │ ├── bootstrap.min.css │ │ │ ├── cerulean.min.css │ │ │ ├── cosmo.min.css │ │ │ ├── flatly.min.css │ │ │ ├── fonts │ │ │ │ ├── Lato.ttf │ │ │ │ ├── LatoBold.ttf │ │ │ │ ├── LatoItalic.ttf │ │ │ │ ├── NewsCycle.ttf │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ ├── OpenSans.ttf │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ ├── Raleway.ttf │ │ │ │ ├── RalewayBold.ttf │ │ │ │ ├── Roboto.ttf │ │ │ │ ├── RobotoBold.ttf │ │ │ │ ├── RobotoLight.ttf │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ └── Ubuntu.ttf │ │ │ ├── journal.min.css │ │ │ ├── lumen.min.css │ │ │ ├── paper.min.css │ │ │ ├── readable.min.css │ │ │ ├── sandstone.min.css │ │ │ ├── simplex.min.css │ │ │ ├── spacelab.min.css │ │ │ ├── united.min.css │ │ │ └── yeti.min.css │ │ ├── fonts │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ └── glyphicons-halflings-regular.woff2 │ │ ├── js │ │ │ ├── bootstrap.js │ │ │ ├── bootstrap.min.js │ │ │ └── npm.js │ │ └── shim │ │ │ ├── html5shiv.min.js │ │ │ └── respond.min.js │ ├── font-awesome-4.5.0 │ │ ├── css │ │ │ ├── font-awesome.css │ │ │ └── font-awesome.min.css │ │ └── fonts │ │ │ └── fontawesome-webfont.ttf │ ├── highlightjs │ │ ├── highlight.null.js │ │ ├── highlight.pack.js │ │ ├── jnbinder.min.css │ │ └── null.min.css │ ├── home.svg │ ├── jnbinder_password.html │ ├── jqueryui-1.11.4 │ │ ├── README │ │ ├── images │ │ │ ├── ui-icons_444444_256x240.png │ │ │ ├── ui-icons_555555_256x240.png │ │ │ ├── ui-icons_777620_256x240.png │ │ │ ├── ui-icons_777777_256x240.png │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ └── ui-icons_ffffff_256x240.png │ │ ├── index.html │ │ ├── jquery-ui.css │ │ ├── jquery-ui.js │ │ ├── jquery-ui.min.css │ │ ├── jquery-ui.min.js │ │ ├── jquery-ui.structure.css │ │ ├── jquery-ui.structure.min.css │ │ ├── jquery-ui.theme.css │ │ └── jquery-ui.theme.min.css │ ├── navigation-1.1 │ │ ├── FileSaver.min.js │ │ ├── codefolding.js │ │ ├── sourceembed.js │ │ └── tabsets.js │ └── tipuesearch │ │ ├── css │ │ ├── normalize.css │ │ └── tipuesearch.css │ │ ├── search.html │ │ ├── search.svg │ │ ├── tipuesearch.js │ │ ├── tipuesearch.min.js │ │ ├── tipuesearch_content.js │ │ └── tipuesearch_set.js ├── variant-annotation.tpl ├── variant-annotation │ └── annovar.html ├── variant-calling.tpl └── variant-calling │ ├── gatk_joint_calling.html │ └── samtools_variant_calling.html ├── fine-mapping ├── README.md ├── SuSiE_RSS_before_initialization.ipynb ├── data │ └── general_annotations.txt ├── finemapping_results_wrangler.ipynb ├── finemapping_to_ldsc.sos ├── gwas_enrichment.ipynb ├── summary_statistics_finemapping.ipynb └── summary_statistics_wrangler.ipynb ├── jnbinder_docker.sh ├── 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